data_2Z09
#
_model_server_result.job_id            RKKsEZBzKw-D01O4QNYzBg 
_model_server_result.datetime_utc      '2025-07-07 11:35:54' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          2z09 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":2001}' 
#
_entry.id    2Z09 
#
_exptl.entry_id    2Z09 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              505.208 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            2Z09 
_cell.length_a            33.22 
_cell.length_b            75.9 
_cell.length_c            88.66 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2Z09 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 33.22 75.9 0 
3 'crystal symmetry operation' 3_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 33.22 0 88.66 
4 'crystal symmetry operation' 4_566 x,-y+1,-z+1 1 0 0 0 -1 0 0 0 -1 0 75.9 88.66 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 D O1A ACP . A ACP 2001 1_555 B MG MG . A MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
metalc ? metalc2 D O2B ACP . A ACP 2001 1_555 B MG MG . A MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
metalc ? metalc3 D O1G ACP . A ACP 2001 1_555 B MG MG . A MG 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
metalc ? metalc4 B MG MG . A MG 3001 1_555 E O HOH . A HOH 3079 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc5 B MG MG . A MG 3001 1_555 E O HOH . A HOH 3080 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc6 B MG MG . A MG 3001 1_555 E O HOH . A HOH 3081 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc7 C MG MG . A MG 3002 1_555 E O HOH . A HOH 3084 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? 
#
_chem_comp.formula           'C11 H18 N5 O12 P3' 
_chem_comp.formula_weight    505.208 
_chem_comp.id                ACP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
PG O1G ACP doub 1 n n 
PG O2G ACP sing 2 n n 
PG O3G ACP sing 3 n n 
PG C3B ACP sing 4 n n 
O2G HOG2 ACP sing 5 n n 
O3G HOG3 ACP sing 6 n n 
PB O1B ACP doub 7 n n 
PB O2B ACP sing 8 n n 
PB C3B ACP sing 9 n n 
PB O3A ACP sing 10 n n 
O2B HOB2 ACP sing 11 n n 
C3B H3B1 ACP sing 12 n n 
C3B H3B2 ACP sing 13 n n 
PA O1A ACP doub 14 n n 
PA O2A ACP sing 15 n n 
PA O3A ACP sing 16 n n 
PA O5' ACP sing 17 n n 
O2A HOA2 ACP sing 18 n n 
O5' C5' ACP sing 19 n n 
C5' C4' ACP sing 20 n n 
C5' "H5'1" ACP sing 21 n n 
C5' "H5'2" ACP sing 22 n n 
C4' O4' ACP sing 23 n n 
C4' C3' ACP sing 24 n n 
C4' H4' ACP sing 25 n n 
O4' C1' ACP sing 26 n n 
C3' O3' ACP sing 27 n n 
C3' C2' ACP sing 28 n n 
C3' H3' ACP sing 29 n n 
O3' HO3' ACP sing 30 n n 
C2' O2' ACP sing 31 n n 
C2' C1' ACP sing 32 n n 
C2' H2' ACP sing 33 n n 
O2' HO2' ACP sing 34 n n 
C1' N9 ACP sing 35 n n 
C1' H1' ACP sing 36 n n 
N9 C8 ACP sing 37 n y 
N9 C4 ACP sing 38 n y 
C8 N7 ACP doub 39 n y 
C8 H8 ACP sing 40 n n 
N7 C5 ACP sing 41 n y 
C5 C6 ACP sing 42 n y 
C5 C4 ACP doub 43 n y 
C6 N6 ACP sing 44 n n 
C6 N1 ACP doub 45 n y 
N6 HN61 ACP sing 46 n n 
N6 HN62 ACP sing 47 n n 
N1 C2 ACP sing 48 n y 
C2 N3 ACP doub 49 n y 
C2 H2 ACP sing 50 n n 
N3 C4 ACP sing 51 n y 
#
_atom_sites.entry_id                     2Z09 
_atom_sites.fract_transf_matrix[1][1]    0.030102 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013175 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.011279 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 MG A 1 3001 3001 MG MG2 . 
C 2 MG A 1 3002 3002 MG MG2 . 
D 3 ACP A 1 2001 2001 ACP ACP . 
E 4 HOH A 1 3003 1 HOH HOH . 
E 4 HOH A 2 3004 2 HOH HOH . 
E 4 HOH A 3 3005 3 HOH HOH . 
E 4 HOH A 4 3006 4 HOH HOH . 
E 4 HOH A 5 3007 5 HOH HOH . 
E 4 HOH A 6 3008 6 HOH HOH . 
E 4 HOH A 7 3009 7 HOH HOH . 
E 4 HOH A 8 3010 8 HOH HOH . 
E 4 HOH A 9 3011 9 HOH HOH . 
E 4 HOH A 10 3012 10 HOH HOH . 
E 4 HOH A 11 3013 11 HOH HOH . 
E 4 HOH A 12 3014 12 HOH HOH . 
E 4 HOH A 13 3015 13 HOH HOH . 
E 4 HOH A 14 3016 14 HOH HOH . 
E 4 HOH A 15 3017 15 HOH HOH . 
E 4 HOH A 16 3018 16 HOH HOH . 
E 4 HOH A 17 3019 17 HOH HOH . 
E 4 HOH A 18 3020 18 HOH HOH . 
E 4 HOH A 19 3021 19 HOH HOH . 
E 4 HOH A 20 3022 20 HOH HOH . 
E 4 HOH A 21 3023 21 HOH HOH . 
E 4 HOH A 22 3024 22 HOH HOH . 
E 4 HOH A 23 3025 23 HOH HOH . 
E 4 HOH A 24 3026 24 HOH HOH . 
E 4 HOH A 25 3027 25 HOH HOH . 
E 4 HOH A 26 3028 26 HOH HOH . 
E 4 HOH A 27 3029 27 HOH HOH . 
E 4 HOH A 28 3030 28 HOH HOH . 
E 4 HOH A 29 3031 29 HOH HOH . 
E 4 HOH A 30 3032 30 HOH HOH . 
E 4 HOH A 31 3033 31 HOH HOH . 
E 4 HOH A 32 3034 32 HOH HOH . 
E 4 HOH A 33 3035 33 HOH HOH . 
E 4 HOH A 34 3036 34 HOH HOH . 
E 4 HOH A 35 3037 35 HOH HOH . 
E 4 HOH A 36 3038 36 HOH HOH . 
E 4 HOH A 37 3039 37 HOH HOH . 
E 4 HOH A 38 3040 38 HOH HOH . 
E 4 HOH A 39 3041 39 HOH HOH . 
E 4 HOH A 40 3042 40 HOH HOH . 
E 4 HOH A 41 3043 41 HOH HOH . 
E 4 HOH A 42 3044 42 HOH HOH . 
E 4 HOH A 43 3045 43 HOH HOH . 
E 4 HOH A 44 3046 44 HOH HOH . 
E 4 HOH A 45 3047 45 HOH HOH . 
E 4 HOH A 46 3048 46 HOH HOH . 
E 4 HOH A 47 3049 47 HOH HOH . 
E 4 HOH A 48 3050 48 HOH HOH . 
E 4 HOH A 49 3051 49 HOH HOH . 
E 4 HOH A 50 3052 50 HOH HOH . 
E 4 HOH A 51 3053 51 HOH HOH . 
E 4 HOH A 52 3054 52 HOH HOH . 
E 4 HOH A 53 3055 53 HOH HOH . 
E 4 HOH A 54 3056 54 HOH HOH . 
E 4 HOH A 55 3057 55 HOH HOH . 
E 4 HOH A 56 3058 56 HOH HOH . 
E 4 HOH A 57 3059 57 HOH HOH . 
E 4 HOH A 58 3060 58 HOH HOH . 
E 4 HOH A 59 3061 59 HOH HOH . 
E 4 HOH A 60 3062 60 HOH HOH . 
E 4 HOH A 61 3063 61 HOH HOH . 
E 4 HOH A 62 3064 62 HOH HOH . 
E 4 HOH A 63 3065 63 HOH HOH . 
E 4 HOH A 64 3066 64 HOH HOH . 
E 4 HOH A 65 3067 65 HOH HOH . 
E 4 HOH A 66 3068 66 HOH HOH . 
E 4 HOH A 67 3069 67 HOH HOH . 
E 4 HOH A 68 3070 68 HOH HOH . 
E 4 HOH A 69 3071 69 HOH HOH . 
E 4 HOH A 70 3072 70 HOH HOH . 
E 4 HOH A 71 3073 71 HOH HOH . 
E 4 HOH A 72 3074 72 HOH HOH . 
E 4 HOH A 73 3075 73 HOH HOH . 
E 4 HOH A 74 3076 74 HOH HOH . 
E 4 HOH A 75 3077 75 HOH HOH . 
E 4 HOH A 76 3078 76 HOH HOH . 
E 4 HOH A 77 3079 77 HOH HOH . 
E 4 HOH A 78 3080 78 HOH HOH . 
E 4 HOH A 79 3081 79 HOH HOH . 
E 4 HOH A 80 3082 80 HOH HOH . 
E 4 HOH A 81 3083 81 HOH HOH . 
E 4 HOH A 82 3084 82 HOH HOH . 
E 4 HOH A 83 3085 83 HOH HOH . 
E 4 HOH A 84 3086 84 HOH HOH . 
E 4 HOH A 85 3087 85 HOH HOH . 
E 4 HOH A 86 3088 86 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 P PG ACP . . . D 3 19.531 34.991 32.229 1 10.62 ? PG ACP 2001 A 1 
HETATM 2 O O1G ACP . . . D 3 18.99 34.16 31.124 1 9.26 ? O1G ACP 2001 A 1 
HETATM 3 O O2G ACP . . . D 3 18.576 35.163 33.493 1 12.89 ? O2G ACP 2001 A 1 
HETATM 4 O O3G ACP . . . D 3 19.874 36.445 31.627 1 14.84 ? O3G ACP 2001 A 1 
HETATM 5 P PB ACP . . . D 3 21.365 32.685 32.831 1 8.19 ? PB ACP 2001 A 1 
HETATM 6 O O1B ACP . . . D 3 22.635 32.377 33.504 1 9.96 ? O1B ACP 2001 A 1 
HETATM 7 O O2B ACP . . . D 3 21.203 32.165 31.331 1 9.59 ? O2B ACP 2001 A 1 
HETATM 8 C C3B ACP . . . D 3 21.133 34.474 32.878 1 10.26 ? C3B ACP 2001 A 1 
HETATM 9 P PA ACP . . . D 3 18.991 31.152 33.386 1 8.02 ? PA ACP 2001 A 1 
HETATM 10 O O1A ACP . . . D 3 18.544 31.364 31.982 1 8.96 ? O1A ACP 2001 A 1 
HETATM 11 O O2A ACP . . . D 3 17.907 31.332 34.527 1 8.61 ? O2A ACP 2001 A 1 
HETATM 12 O O3A ACP . . . D 3 20.209 32.114 33.794 1 6.79 ? O3A ACP 2001 A 1 
HETATM 13 O O5' ACP . . . D 3 19.602 29.669 33.55 1 7.99 ? O5' ACP 2001 A 1 
HETATM 14 C C5' ACP . . . D 3 19.321 28.777 34.637 1 8.04 ? C5' ACP 2001 A 1 
HETATM 15 C C4' ACP . . . D 3 18.723 27.496 34.047 1 5.05 ? C4' ACP 2001 A 1 
HETATM 16 O O4' ACP . . . D 3 17.448 27.75 33.426 1 7.03 ? O4' ACP 2001 A 1 
HETATM 17 C C3' ACP . . . D 3 19.532 26.857 32.916 1 7.02 ? C3' ACP 2001 A 1 
HETATM 18 O O3' ACP . . . D 3 20.629 26.071 33.394 1 8.17 ? O3' ACP 2001 A 1 
HETATM 19 C C2' ACP . . . D 3 18.476 25.905 32.34 1 6.17 ? C2' ACP 2001 A 1 
HETATM 20 O O2' ACP . . . D 3 18.267 24.765 33.183 1 7.5 ? O2' ACP 2001 A 1 
HETATM 21 C C1' ACP . . . D 3 17.191 26.734 32.436 1 6.65 ? C1' ACP 2001 A 1 
HETATM 22 N N9 ACP . . . D 3 16.883 27.47 31.184 1 5.94 ? N9 ACP 2001 A 1 
HETATM 23 C C8 ACP . . . D 3 17.259 28.702 30.836 1 7.42 ? C8 ACP 2001 A 1 
HETATM 24 N N7 ACP . . . D 3 16.841 28.928 29.593 1 9.63 ? N7 ACP 2001 A 1 
HETATM 25 C C5 ACP . . . D 3 16.201 27.843 29.151 1 7.55 ? C5 ACP 2001 A 1 
HETATM 26 C C6 ACP . . . D 3 15.598 27.489 27.948 1 7.17 ? C6 ACP 2001 A 1 
HETATM 27 N N6 ACP . . . D 3 15.609 28.29 26.873 1 8.83 ? N6 ACP 2001 A 1 
HETATM 28 N N1 ACP . . . D 3 15.08 26.252 27.883 1 6.29 ? N1 ACP 2001 A 1 
HETATM 29 C C2 ACP . . . D 3 15.106 25.387 28.893 1 6.91 ? C2 ACP 2001 A 1 
HETATM 30 N N3 ACP . . . D 3 15.661 25.689 30.06 1 5.53 ? N3 ACP 2001 A 1 
HETATM 31 C C4 ACP . . . D 3 16.217 26.91 30.179 1 8.05 ? C4 ACP 2001 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           326 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#